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Increasing bioinformatics in third world countries: Studies of S.digitata and P.Polymyxa to further bioinformatics in east Africa
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. (SLU Global Bioinformatics Centre)
2016 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Bioinformatiska förbättringsåtgärder för u-länder : Studier av S.digitata och P.Polymyxa för att förbättra bioinformatiken i östra Afrika (Swedish)
Abstract [en]

Despite an increase of biotechnical studies in third world countries, the bioinformatical side is largely lacking. In this paper we attempt to further the bioinformatical capabilities of east Af-rica. The project consisted of two teaching segments for east African doctorates, one as part of an academic workshop at ILRI, Kenya, and one in a small class at SLU, Sweden. The project also included the generation of two simple to use bioinformatical pipelines with the explicit aim to be reused by novice bioinformaticians from the very same region. The viability of the piplines were verified by generating transcriptional expression level differences for Paeni-bacillus polymyxa strain A26 and whole genome annotations for Setaria digitata. Both pipe-lines may have some merit for the collaborative effort between ILRI and SLU to annotate Eleusine coracana, a draught resilient crop, the annotation of which may save lives. The teaching material, source code for the pipelines and overall teaching impression have been included in this paper.

Place, publisher, year, edition, pages
2016. , 59 p.
UPTEC X, 15 034
Keyword [en]
bioinformatics, pipeline, Setaria digitata, Paenibacillus polymyxa, Eleusine coracana, annotation, expression level, east Africa, eBioKit, MAKER, Cufflinks, third world country, genome, transcriptome
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:uu:diva-293636OAI: diva2:928095
Educational program
Molecular Biotechnology Engineering Programme
2015-10-15, BMC, Husargatan 3, Uppsala, 13:42 (English)
Available from: 2016-05-16 Created: 2016-05-14 Last updated: 2016-05-16Bibliographically approved

Open Access in DiVA

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